The Edwards Aquifer (EA) is the source of major springs, containing numerous listed aquatic species and the sole source of water for 2 million central Texans. Mining of aquifers is a threat to all EA spring ecosystems and is the focus of several attempted regional scale HCPs. Yet many springs with listed species occur in the center of urban environments and face localized, spring-specific threats due to urbanization, pollution and exotic species. The San Marcos River HCP (SMRHCP) is localized within a regional context and evaluates proposed projects as potential threats to endangered species in the river, modifies existing projects to reduce threat and requires mitigation for potential take. SMRHCP uses a science-based ecological approach to address problems and optimize solutions in the management of exotic vegetation to enhance recreation and removal of silt due to urban growth and flood control structures. The SMRHCP requires a localized watershed management and recreation master plans and also establishes a partnership between city, state, and federal agencies that has promoted communication and cooperation that previously did not exist. Smaller-scale HCPs may be effective management and conservation tools to deal with localized environmental issues, while more spatially and stakeholder complex plans are developed.